Feature counts error

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1

I was trying to run a workflow but ran into some problems, which I think are related to featurecounts. Basically, once instance of featurecounts in a workflow>it runs. Two instances in a workflow>it does not run. Remove either featurecount from the workflow>it runs again. These kinds of problems do not occur if I use htseq instead, but I would prefer to use featurecounts because it counts more reads that are of interest to me.

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Hi @cjain
I tested a workflow with two featureCounts, the same input files, but different settings (gene_id vs gene_name for count aggregation) and cannot reproduce the issue. What do you mean by ‘workflow does not run’? Some jobs fail or you don’t see outputs? Make sure that you ‘activated’ output files in the workflow or check hidden files.
Kind regards,
Igor

3

Hi Igor,

Thank you for looking into this issue. What I meant is that if I have two featurecounts each of which have the same GFF gene identifier but different GFF feature types (e.g., tRNA and rRNA), then when I press the “run workflow” button, the workflow does not get activated. However, if I delete either featurecount module and press the “run workflow” button, the workflow starts right away.

If you have been able to get a workflow with two featurecount modules to run, is it possible to send it to me so that I can compare your workflow with mine? Perhaps there is something about my choice of options that is preventing my workflow from working properly.

Thanks,

cjain

4

Hi @cjain
thank you for the additional description. I never experiences the situation you’ve described.
My workflow:
https://usegalaxy.org.au/u/igor/w/featurecountstest
The outputs of featureCounts jobs were renamed based on alignment file plus label for 1st or 2nd job. For the best experience use a BAM file named something like sample_name.bam.
in both featureCounts jobs the reads were counted for ‘exon’ and aggregated on gene_id and gene_name, respectively.
Kind regards,
Igor

5

Hi @cjain
have you checked the annotation file for presence of rRNA and rRNA features? Can you run featureCounts on both settings?
I submitted my workflow with two featureCounts, 1st: exon and gene_id; 2nd: gene and gene_name, and it was completed.
Kind regards,
Igor

6

Hi Igor,

I tried your workflow and it runs fine. Your workflow has inputs that are configured somewhat differently from mine, which might be the reason why yours worked and mine did not. Thank you for your time!

Regards,

Chaitanya

7

Hi Chaitanya,
I’ve built the workflow ‘from scratch’ in Workflow editor. Just add two input boxes, for alignment and annotation, add meaningful description, add tools, and you’ll be fine.
Kind regards,
Igor

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